Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020675.1 Corchorus olitorius cultivar O-4 contig20708, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 9902
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:1643 original size:24 final size:26

Alignment explanation


    Indices: 1598--1646  Score: 75
    Period size: 24  Copynumber: 2.0  Consensus size: 26

       1588 ACAATTTTTT

                *                     
       1598 TTTGTTATAATTATTTTAAAAATTTC
          1 TTTGATATAATTATTTTAAAAATTTC

                                     
       1624 TTTGATAT-ATTA-TTTAAAAATTT
          1 TTTGATATAATTATTTTAAAAATTT

       1647 TCTAACCAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24   11  0.50
  25    4  0.18
  26    7  0.32

ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57


Consensus pattern (26 bp):   
TTTGATATAATTATTTTAAAAATTTC

Found at i:1643 original size:25 final size:26

Alignment explanation


    Indices: 1598--1649  Score: 70
    Period size: 25  Copynumber: 2.0  Consensus size: 26

       1588 ACAATTTTTT

                *           *         
       1598 TTTGTTATAATTATTTTAAAAATTTC
          1 TTTGATATAATTATTTAAAAAATTTC

                                 *    
       1624 TTTGATAT-ATTATTTAAAAATTTTC
          1 TTTGATATAATTATTTAAAAAATTTC

             
       1649 T
          1 T

       1650 AACCAAAATT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  25   16  0.70
  26    7  0.30

ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58


Consensus pattern (26 bp):   
TTTGATATAATTATTTAAAAAATTTC

Found at i:4119 original size:76 final size:76

Alignment explanation


    Indices: 3975--4126  Score: 175
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       3965 ACAAGGACGC

                                                               *        *  * 
       3975 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCTAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
       4040 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *               *                           **     
       4051 CGACTCCAGCTGGGTGCCCACATGGTTTG-TTTGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                   *      
       4113 GATGGGCTGTGTCA
         63 GATGGGCAGTGTCA

       4127 TAGCTCATCA


Statistics
Matches: 64,  Mismatches: 9, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
  75    4  0.06
  76   55  0.86
  77    5  0.08

ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Done.